spacer
spacer

PDBsum entry 2yv9

Go to PDB code: 
protein metals Protein-protein interface(s) links
Metal transport PDB id
2yv9
Jmol
Contents
Protein chains
285 a.a. *
266 a.a. *
Metals
_CA ×2
Waters ×344
* Residue conservation analysis
PDB id:
2yv9
Name: Metal transport
Title: Crystal structure of the clic homologue exc-4 from c. Elegans
Structure: Chloride intracellular channel exc-4. Chain: a, b. Synonym: excretory canal abnormal protein 4. Engineered: yes
Source: Caenorhabditis elegans. Organism_taxid: 6239. Gene: exc-4. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.60Å     R-factor:   0.190     R-free:   0.235
Authors: S.J.Harrop,D.R.Littler,P.M.G.Curmi
Key ref:
D.R.Littler et al. (2008). Comparison of vertebrate and invertebrate CLIC proteins: the crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC. Proteins, 71, 364-378. PubMed id: 17985355 DOI: 10.1002/prot.21704
Date:
10-Apr-07     Release date:   19-Feb-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8WQA4  (EXC4_CAEEL) -  Chloride intracellular channel exc-4
Seq:
Struc:
290 a.a.
285 a.a.
Protein chain
Pfam   ArchSchema ?
Q8WQA4  (EXC4_CAEEL) -  Chloride intracellular channel exc-4
Seq:
Struc:
290 a.a.
266 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   8 terms 
  Biological process     transport   7 terms 
  Biochemical function     voltage-gated ion channel activity     2 terms  

 

 
DOI no: 10.1002/prot.21704 Proteins 71:364-378 (2008)
PubMed id: 17985355  
 
 
Comparison of vertebrate and invertebrate CLIC proteins: the crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC.
D.R.Littler, S.J.Harrop, L.J.Brown, G.J.Pankhurst, A.V.Mynott, P.Luciani, R.A.Mandyam, M.Mazzanti, S.Tanda, M.A.Berryman, S.N.Breit, P.M.Curmi.
 
  ABSTRACT  
 
The crystal structures of two CLIC family members DmCLIC and EXC-4 from the invertebrates Drosophila melanogaster and Caenorhabditis elegans, respectively, have been determined. The proteins adopt a glutathione S-transferase (GST) fold. The structures are highly homologous to each other and more closely related to the known structures of the human CLIC1 and CLIC4 than to GSTs. The invertebrate CLICs show several unique features including an elongated C-terminal extension and a divalent metal binding site. The latter appears to alter the ancestral glutathione binding site, and thus, the invertebrate CLICs are unlikely to bind glutathione in the same manner as the GST proteins. Purified recombinant DmCLIC and EXC-4 both bind to lipid bilayers and can form ion channels in artificial lipid bilayers, albeit at low pH. EXC-4 differs from other CLIC proteins in that the conserved redox-active cysteine at the N-terminus of helix 1 is replaced by an aspartic acid residue. Other key distinguishing features of EXC-4 include the fact that it binds to artificial bilayers at neutral pH and this binding is not sensitive to oxidation. These differences with other CLIC family members are likely to be due to the substitution of the conserved cysteine by aspartic acid.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Cartoon representation of DmCLIC and EXC-4 structures. Cartoon representations of the backbone structures of A: DmCLIC in stereo. B: The A subunit of EXC-4 in the P2[1] crystal form in stereo. C: Human CLIC1. D: Backbone alignment of the DmCLIC (purple) and CLIC4(ext) (green) crystal structures. E: Orthogonal views of the EXC-4 dimer as seen in the asymmetric unit of the crystal structure. In each cartoon panel, helices shown in red (except in the dimer, where blue is used for the B subunit), -strands in yellow and loop regions in green. Breaks in electron density are shown with dotted magenta lines. Secondary structural elements and the N- and C-termini are labeled.
Figure 4.
Figure 4. Redox and divalent cation sites. Ball and stick representation of the redox active motifs at the N-terminus of helix 1 in A: the reduced CLIC1 monomer, B: the reduced DmCLIC monomer and C: the reduced EXC-4 monomer structures. The side chains of residues within the respective CxxS, CxxC, and DxxC motifs are shown. Hydrogen bonds within helix 1 are represented with dashed purple lines. D: The bound calcium ion (shown as a purple sphere) in located between -strand 3 and helix 3. The cis-proline (Pro-85) at the N-terminus of -strand 3 is conserved in proteins containing the GST-fold. The side chains of residues 83-87, 95, and 97 are shown and labeled, the side chains of Cys-40 and Cys-43 are shown but unlabelled (upper right). The ligand interactions to the bound calcium ion are represented as purple dashed lines. E: Location of redox active motif in DmCLIC, as shown in B.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 364-378) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21469130 G.He, Y.Ma, S.Y.Chou, H.Li, C.Yang, J.Z.Chuang, C.H.Sung, and A.Ding (2011).
Role of CLIC4 in the host innate responses to bacterial lipopolysaccharide.
  Eur J Immunol, 41, 1221-1230.  
19247789 J.J.Tung, O.Hobert, M.Berryman, and J.Kitajewski (2009).
Chloride intracellular channel 4 is involved in endothelial proliferation and morphogenesis in vitro.
  Angiogenesis, 12, 209-220.  
19650640 S.H.Stoychev, C.Nathaniel, S.Fanucchi, M.Brock, S.Li, K.Asmus, V.L.Woods, and H.W.Dirr (2009).
Structural dynamics of soluble chloride intracellular channel protein CLIC1 examined by amide hydrogen-deuterium exchange mass spectrometry.
  Biochemistry, 48, 8413-8421.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.